LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
package gpu 0
# 3d soft repulsive particles

units           real
atom_style      atomic

lattice         fcc 5.0 origin 0.1 0.1 0.1
Lattice spacing in x,y,z = 5 5 5
region          box block -5 5 -5 5 -5 5
create_box      2 box
Created orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 1 by 1 MPI processor grid
create_atoms    1 box
Created 4000 atoms
  using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
  create_atoms CPU = 0.000 seconds
set type 1 type/ratio 2 0.5 424662346
Setting atom values ...
  2000 settings made for type/ratio
mass            * 1.0

velocity        all create 3.0 87287

pair_style      python 9.0
pair_coeff      * * py_pot.Harmonic A B

neighbor        1.0 bin
neigh_modify    every 2 delay 4 check yes

fix             1 all nve

thermo          50
run             250 post no

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- GPU package (short-range, long-range and three-body potentials):

@Article{Brown11,
 author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},
 title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},
 journal = {Comp.~Phys.~Comm.},
 year =    2011,
 volume =  182,
 pages =   {898--911}
}

@Article{Brown12,
 author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},
 title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},
 journal = {Comp.~Phys.~Comm.},
 year =    2012,
 volume =  183,
 pages =   {449--459}
}

@Article{Brown13,
 author = {W. M. Brown, Y. Masako},
 title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},
 journal = {Comp.~Phys.~Comm.},
 year =    2013,
 volume =  184,
 pages =   {2785--2793}
}

@Article{Trung15,
 author = {T. D. Nguyen, S. J. Plimpton},
 title = {Accelerating dissipative particle dynamics simulations for soft matter systems},
 journal = {Comput.~Mater.~Sci.},
 year =    2015,
 volume =  100,
 pages =   {173--180}
}

@Article{Trung17,
 author = {T. D. Nguyen},
 title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},
 journal = {Comp.~Phys.~Comm.},
 year =    2017,
 volume =  212,
 pages =   {113--122}
}

@Article{Nikolskiy19,
 author = {V. Nikolskiy, V. Stegailov},
 title = {GPU acceleration of four-site water models in LAMMPS},
 journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},
 year =    2019
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 2 steps, delay 4 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair python, perpetual
      attributes: half, newton off
      pair build: half/bin/newtoff
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.612 | 4.612 | 4.612 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            3    423789.56            0    423825.32     249259.3 
      50    75.889551    422919.46            0    423824.08    248893.24 
     100    105.20972    422570.47            0     423824.6     250756.6 
     150    132.08764    422249.71            0    423824.23    251894.29 
     200    118.14116    422416.43            0     423824.7    252088.96 
     250    128.40086    422293.71            0    423824.28    252057.16 
Loop time of 21.1837 on 1 procs for 250 steps with 4000 atoms


write_restart   repulsive.restart
System init for write_restart ...
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule

clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
package gpu 0

read_restart    repulsive.restart
Reading restart file ...
  restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
  restoring atom style atomic from restart
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 1 by 1 MPI processor grid
  pair style python stores no restart info
  4000 atoms
  read_restart CPU = 0.000 seconds

pair_style      python 10.0
pair_coeff      * * py_pot.Harmonic A B

shell rm -f python.dat
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
Creating table file python.dat with DATE: 2022-03-18
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 9 9 9
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair python, perpetual
      attributes: half, newton off
      pair build: half/bin/newtoff
      stencil: full/bin/3d
      bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
Appending to table file python.dat with DATE: 2022-03-18
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
Appending to table file python.dat with DATE: 2022-03-18
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule

fix             1 all nve

thermo          50
run             250 post no
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.451 | 5.451 | 5.451 Mbytes
Step Temp E_pair E_mol TotEng Press 
     250    128.40086    422293.71            0    423824.28    252057.16 
     300    119.72871     422397.4            0     423824.6    251985.11 
     350    124.88375    422335.77            0    423824.42    252051.28 
     400    121.76143    422373.11            0    423824.53    252006.39 
     450    125.29847     422330.9            0    423824.49    251997.23 
     500    126.87408    422312.08            0    423824.45    252053.51 
Loop time of 28.5184 on 1 procs for 250 steps with 4000 atoms


clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
package gpu 0

read_restart    repulsive.restart
Reading restart file ...
  restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
  restoring atom style atomic from restart
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 1 by 1 MPI processor grid
  pair style python stores no restart info
  4000 atoms
  read_restart CPU = 0.000 seconds

pair_style      harmonic/cut
pair_coeff      1 1 0.2 9.0
pair_coeff      2 2 0.4 9.0

shell rm -f harmonic.dat
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
Creating table file harmonic.dat with DATE: 2022-03-18
  generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 11
  ghost atom cutoff = 11
  binsize = 5.5, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair harmonic/cut, perpetual
      attributes: half, newton off
      pair build: half/bin/newtoff
      stencil: full/bin/3d
      bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
Appending to table file harmonic.dat with DATE: 2022-03-18
  generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
Appending to table file harmonic.dat with DATE: 2022-03-18
  generated 1 of 1 mixed pair_coeff terms from geometric mixing rule

neighbor        1.0 bin
neigh_modify    every 2 delay 4 check yes

fix             1 all nve

thermo          50
run             250 post no
  generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
Step Temp E_pair E_mol TotEng Press 
     250    128.40086    422293.71            0    423824.28    252057.16 
     300    119.72871     422397.4            0     423824.6    251985.11 
     350    124.88375    422335.77            0    423824.42    252051.28 
     400    121.76143    422373.11            0    423824.53    252006.39 
     450    125.29847     422330.9            0    423824.49    251997.23 
     500    126.87408    422312.08            0    423824.45    252053.51 
Loop time of 1.1146 on 1 procs for 250 steps with 4000 atoms


clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
package gpu 0

read_restart    repulsive.restart
Reading restart file ...
  restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
  restoring atom style atomic from restart
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 1 by 1 MPI processor grid
  pair style python stores no restart info
  4000 atoms
  read_restart CPU = 0.000 seconds

pair_style      table spline 1000
pair_coeff      1 1 python.dat PYTH_A_A
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff      1 2 python.dat PYTH_A_B
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff      2 2 python.dat PYTH_B_B
Reading pair table potential file python.dat with DATE: 2022-03-18

neighbor        1.0 bin
neigh_modify    every 2 delay 4 check yes

fix             1 all nve

thermo          50
run             250 post no
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes
Step Temp E_pair E_mol TotEng Press 
     250    128.40086    422293.71            0    423824.28    252057.14 
     300    119.72876     422397.4            0     423824.6    251985.09 
     350    124.88381    422335.77            0    423824.42    252051.26 
     400    121.76148    422373.11            0    423824.53    252006.37 
     450    125.29841     422330.9            0    423824.49     251997.2 
     500    126.87418    422312.08            0    423824.45    252053.48 
Loop time of 0.389958 on 1 procs for 250 steps with 4000 atoms


# remove temporary files
shell rm repulsive.restart harmonic.dat python.dat
Total wall time: 0:00:54
